I have gone into space and went EVA and right clicked on my kerbal, nothing appeared. (I am in science mode) I can't use the mystery goo container or science jr. I am on a mac and using 1.0.4.
The only time you want to EVA regarding science experiments (aside from the obvious crew reports/surface samples/flags/etc) is to collect data for storage. With a kerbal in the command pod, right click on your thermometer, pressure sensor, etc., and run the experiments. You can either transmit them from there, or if you want to keep the data (usually for a higher science return) you can then EVA to collect the data, which requires proximity to the experiment item. Once you get close enough to the Science Jr., for example, you can right click and "Collect Data", then go back near the command module and right click on it to store the data. This allows your command module to hold data from the same experiment in different biomes for example, increasing your overall science output.
A scientist also has to reset certain experiments (like the Science Jr and Mystery Goo canisters) in order for them to be used again. That also requires an EVA, but can be done immediately after collecting the data from that experiment.
tl;dr: Don't EVA to perform the experiments, just run the experiments with the kerbal in the command module, then you can EVA to collect the data and/or reset the experiments.
I understand your question but it is phrased poorly.
In my KSP saves, I cannot be in EVA in order to use scientific instruments on the spacecraft (the Mystery Goo and Science Junior are both spacecraft items, and thus can only be controlled when you are playing as THAT spacecraft only.)
You can use EVA to perform scientific experiments on the surface of a planet (gathering samples). For this you right-click your Kerbal and select "Collect Samples" (or something on those lines.)
If you want a crew report, right click on the cockpit of your craft and select "Crew Report". This gives a moderate amount of science.
Every time you repeat a scientific experiment, it gives less science (lets say you are on the Kerbin coast playing with Mystery Goo and it gives you 8 science the first time, it will give you 2 the next, etc.
Hope this helps.